Proton pump inhibitor（PPI）was widely used in clinic as a first-line drug for the treatment of gastroesophageal reflux disease and peptic ulcer. As the most commonly used prescription drug in digestive department，its usage is increasing year by year. With the long-term use of drugs，a variety of adverse reactions had been reported in recent years. Several studies had shown that use of PPI would cause the disorder of gastrointestinal flora，and was positively correlated with increased risk of intestinal infection. This paper summarized the correlation between PPI and gastrointestinal flora.